gg_KM <- function(fit,title="",legend="none",confinterval=TRUE,startPoint=FALSE,cumIncidence=FALSE,censorSize=1,stepSize=1,background=TRUE,ticks="1x",ylabel="surv",xlabel="time",colors=c(),pval=data.frame(text="",x="",y="",stringsAsFactors = FALSE),x_limit=NULL, namesOfStrata = c(), timeInYears = FALSE,legendTitle=""){
require(scales)
require(grid)
require(ggplot2)
require(survival)
#bad solution, fix soon
if(cumIncidence){
fit[["surv"]]=1-fit[["surv"]]
fit[["lower"]]=1-fit[["lower"]]
fit[["upper"]]=1-fit[["upper"]]
}
nrTicks=switch(ticks,"1x"=1,"2x"=2,"4x"=4)
if(timeInYears){
fit$time=fit$time/365.25
}
legend_position=switch(legend,"none"="none","top-right"=c(1,1),"bottom-right"=c(1,0),"top-left"=c(0,1),"bottom-left"=c(0,0))
f.frame=as.data.frame(with(fit,cbind(time,n.risk,n.event,n.censor,surv,upper,lower)))
if(!"strata" %in% names(fit)){
f.frame$strata=factor("Overall")
namesOfStrata="Overall"
#levels(fit$strata)="Overall"
}else {
if(length(namesOfStrata) == 0){
namesOfStrata = names(fit$strata)
}else{
names(fit$strata)=namesOfStrata
}
strata=rep(namesOfStrata,fit$strata)
f.frame$strata=factor(strata,levels=namesOfStrata,ordered = TRUE)
}
if(startPoint==FALSE){
zeros=rep(0,nlevels(f.frame$strata))
#Take into account if user wants to plot cumulative incidence
startValue=ifelse(cumIncidence,rep(0,nlevels(f.frame$strata)),rep(1,nlevels(f.frame$strata)))
start=data.frame("time"=zeros,"n.risk"=fit$n,"n.event"=zeros,"n.censor"=zeros,"surv"=startValue,"upper"=startValue,"lower"=startValue,"strata"=factor(namesOfStrata,levels=namesOfStrata,ordered=TRUE))
f.frame=rbind(start,f.frame)
}
f.frame=f.frame[with(f.frame,order(strata,time)),]
g=ggplot(data=f.frame,aes(time,surv))+geom_step(aes(time,surv,colour=strata),size=stepSize,direction="hv",na.rm=TRUE)+
geom_point(data=subset(f.frame, n.censor > 0), aes(x=time, y=surv),size=censorSize,shape=3,na.rm=TRUE)+theme_bw()+
ggtitle(title)+ylab(ylabel)+xlab(xlabel)+ylim(0,1) + scale_color_discrete(name=legendTitle) +
theme(
title = element_text(vjust=2),
legend.position=legend_position,
legend.justification=legend_position,
legend.background = element_rect(linetype = 1,colour="black",size=0.2),
axis.title.x=element_text(vjust=0),
axis.line = element_line(color = 'black'),
plot.margin = unit(c(1,1,0.2, 1),"cm"))
if(confinterval){
g=g+geom_step(aes(time,upper,colour=strata),direction="hv",linetype="dashed",na.rm=TRUE)+
geom_step(aes(time,lower,colour=strata),direction="hv",linetype="dashed",na.rm=TRUE)
}
if(!background){
g=g+theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_line(color = "black"),
panel.border = element_blank()
)
}
if(length(colors)!=0){
g=g+scale_colour_manual(name=legendTitle,values=colors)
}
if(!is.na(as.numeric(pval$x)) && nchar(pval)!=0){
g=g+geom_text(data=pval,aes(x,y,label=text),na.rm=TRUE)
}
if(is.null(x_limit)){
x_limit=c(min(fit$time),max(fit$time))
}
g=g+scale_x_continuous(limits=x_limit)
xticks=ggplot_build(g)$panel$ranges[[1]]$x.major_source
#Extract the right end of x axis
xmax= ggplot_build(g)$panel$ranges[[1]]$x.range[2]
#adding xticks and making sure they are non negative
g=g+scale_x_continuous(limits=x_limit,breaks = pretty(c(min(fit$time),xmax),length(xticks)*nrTicks))
xticks=ggplot_build(g)$panel$ranges[[1]]$x.major_source
if(!"strata" %in% names(fit)){
summarystrata=rep(factor("Overall"),length(xticks))
}else{
summarystrata=summary(fit, times = xticks, extend = TRUE)$strata
}
risk.data <- data.frame(strata = summarystrata,
time = summary(fit, times = xticks, extend = TRUE)$time,
n.risk = summary(fit, times = xticks, extend = TRUE)$n.risk)
return(list("plot"=g,"risk.data"=risk.data,"f.frame"=f.frame,x_limit=x_limit))
}
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